Variant report

Variant	rs1143678
Chromosome Location	chr16:31343005-31343006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31341937..31343785-chr16:31345527..31347045,2	K562	blood:
2	chr16:31340966..31343264-chr16:31454013..31455624,2	MCF-7	breast:
3	chr16:31308392..31310591-chr16:31341817..31344039,2	K562	blood:
4	chr16:31342392..31343986-chr16:31347244..31349142,2	MCF-7	breast:
5	chr16:31225253..31228025-chr16:31342774..31345764,2	MCF-7	breast:
6	chr16:31190368..31193316-chr16:31342467..31345225,2	K562	blood:
7	chr16:31331494..31335412-chr16:31342610..31345111,3	K562	blood:
8	chr16:31118693..31121313-chr16:31341607..31344535,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000089280	Chromatin interaction
ENSG00000177238	Chromatin interaction
ENSG00000252809	Chromatin interaction
ENSG00000169900	Chromatin interaction
ENSG00000176723	Chromatin interaction
ENSG00000103507	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11150615	1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1143679	1.00[ASN][1000 genomes]
rs1143683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11574636	1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11574637	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs11859300	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11859349	1.00[ASN][1000 genomes]
rs11860650	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs11861161	1.00[ASN][1000 genomes]
rs11864503	1.00[ASN][1000 genomes]
rs11864541	1.00[ASN][1000 genomes]
rs11864813	1.00[ASN][1000 genomes]
rs11865746	1.00[ASN][1000 genomes]
rs12102768	1.00[ASN][1000 genomes]
rs12103025	1.00[ASN][1000 genomes]
rs12917874	1.00[ASN][1000 genomes]
rs12920597	1.00[ASN][1000 genomes]
rs12928725	1.00[ASN][1000 genomes]
rs12928810	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13331557	1.00[ASN][1000 genomes]
rs13338069	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs28385574	1.00[ASN][1000 genomes]
rs28773820	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28821928	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs28825532	1.00[ASN][1000 genomes]
rs28834423	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28855735	1.00[ASN][1000 genomes]
rs34082782	1.00[ASN][1000 genomes]
rs34572943	1.00[ASN][1000 genomes]
rs34767000	1.00[ASN][1000 genomes]
rs34770440	1.00[ASN][1000 genomes]
rs35314490	1.00[ASN][1000 genomes]
rs35383035	1.00[ASN][1000 genomes]
rs35472514	1.00[ASN][1000 genomes]
rs36001237	1.00[ASN][1000 genomes]
rs36055763	1.00[ASN][1000 genomes]
rs41476751	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4548893	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs4632147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58408589	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59559257	1.00[ASN][1000 genomes]
rs60312440	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6565227	1.00[ASN][1000 genomes]
rs6565228	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs67898294	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71390269	1.00[ASN][1000 genomes]
rs71391210	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7184339	1.00[ASN][1000 genomes]
rs7184677	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7187713	1.00[ASN][1000 genomes]
rs7190018	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs7190807	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7192039	1.00[ASN][1000 genomes]
rs7193268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7198598	1.00[ASN][1000 genomes]
rs7199496	1.00[ASN][1000 genomes]
rs7199532	1.00[ASN][1000 genomes]
rs7200615	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7204735	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206312	1.00[ASN][1000 genomes]
rs73534420	1.00[ASN][1000 genomes]
rs7499077	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs8056276	1.00[ASN][1000 genomes]
rs8056944	1.00[ASN][1000 genomes]
rs9745421	1.00[ASN][1000 genomes]
rs9888739	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs9888879	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs9922766	1.00[ASN][1000 genomes]
rs9923357	1.00[ASN][1000 genomes]
rs9923767	1.00[ASN][1000 genomes]
rs9928372	1.00[ASN][1000 genomes]
rs9928749	1.00[ASN][1000 genomes]
rs9930524	1.00[ASN][1000 genomes]
rs9933520	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9933937	1.00[ASN][1000 genomes]
rs9936831	1.00[ASN][1000 genomes]
rs9937645	1.00[ASN][1000 genomes]
rs9937837	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9938063	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[ASN][1000 genomes]
rs9939679	1.00[ASN][1000 genomes]
rs9940397	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059459	chr16:31299088-31462251	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv542901	chr16:31299088-31462251	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
4	nsv1058992	chr16:31337455-31414881	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv542902	chr16:31337455-31414881	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1061980	chr16:31338462-31415471	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1143678	FUS	cis	cerebellum	SCAN
rs1143678	ITGAM	cis	lymphoblastoid	seeQTL
rs1143678	FAM57B	cis	parietal	SCAN
rs1143678	HIRIP3	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31323000-31344600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr16:31341200-31343200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr16:31341400-31343400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
4	chr16:31341800-31343200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr16:31341800-31343200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr16:31342000-31343400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr16:31342000-31343400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr16:31342200-31343200	Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr16:31342200-31343200	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr16:31342400-31343200	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr16:31342400-31343200	Active TSS	Primary T cells from cord blood	blood
12	chr16:31342400-31343200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
13	chr16:31342400-31343200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
14	chr16:31342400-31343200	Active TSS	Right Ventricle	heart
15	chr16:31342400-31343200	Genic enhancers	Spleen	Spleen
16	chr16:31342400-31343200	Active TSS	A549	lung
17	chr16:31342400-31343400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr16:31342400-31343400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
19	chr16:31342400-31343400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
20	chr16:31342600-31343200	Active TSS	Primary B cells from cord blood	blood
21	chr16:31342600-31343200	Active TSS	Thymus	Thymus
22	chr16:31342600-31343200	Bivalent/Poised TSS	HSMM	muscle
23	chr16:31342600-31343400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr16:31342800-31343200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr16:31342800-31343200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr16:31342800-31343200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr16:31342800-31343200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr16:31342800-31343200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr16:31342800-31343200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr16:31342800-31343200	Flanking Bivalent TSS/Enh	Dnd41	blood
31	chr16:31342800-31343200	Bivalent/Poised TSS	HepG2	liver
32	chr16:31342800-31343400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
33	chr16:31342800-31343400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
34	chr16:31342800-31344200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr16:31342800-31344400	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr16:31343000-31343200	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:31343000-31343200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr16:31343000-31343200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr16:31343000-31343200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
40	chr16:31343000-31343200	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr16:31343000-31343200	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
42	chr16:31343000-31343200	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr16:31343000-31343200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
44	chr16:31343000-31343200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr16:31343000-31343200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr16:31343000-31343200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr16:31343000-31343200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr16:31343000-31343200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr16:31343000-31343200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
50	chr16:31343000-31343200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin

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